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It's the reverse of Surface_Abstraction_Beta_vdW, which is better named and has some data.
The family has been removed. Delete it's png
…ismGenerator/new_surface_families
…r#629) Total recalculation of adsorption energies (except things adsorbing through an N atom), forming into new trees. Greatly improves bidentate binding energies. Results probably quite different, hopefully much better. @bjkreitz wrote: I completely overhauled the adsorption correction database for Pt(111). The current [previous] adsorption corrections are based on the initial Pt(111) database create by Katrin (DOI:10.1021/acs.iecr.9b01464). I have updated the adsorption corrections to include all the adsorbates that I have added recently (DOI: 10.1021/acscatal.2c03378). Additionally, I have revised the thermo tree for bidentate and included a new branch for bridged bidentate species. The new adsorption correction trees can be found in the SI of this paper DOI: 10.1002/anie.202306514. Our previous adsorption correction for the enthalpy of formation for bidentate species was a simple addition of two monodentate corrections. This is grossly wrong (usually a few hundred kJ/mol). In order to provide better estimates, I have averaged the corrections for all species that are at a specific node. Higher level nodes are averaged over all children. I have not touched the adsorption corrections for adsorbates containing N.
…#628) Update list of default surface reaction families and restrict Abstraction_Single_vdW. 1. Turn off the reaction families for which we currently only have made up rules or a single training reactions in the recommended.py file by default. The reactions include Surface_EleyRideal_Addition_Multiple_Bond, Surface_Migration, Surface_DoubleBond_to_Bidentate, and Surface_Addition_Single_vdW. We anticipate that the elementary steps discovered by these families will cause problems in the microkinetic models due to the unreasonable rate estimates. 2. Additionally, we restricted the Surface_Abstraction_Single_vdW to not abstract other atoms with an adsorbed H and removed physisorbed H2 from the tree (see discussion #2494) 3. We updated the top level BEP rule of Surface_Abstraction_Single_vdW with the BEP from Surface_Abstraction_Beta_vdW to provide better rate estimates.
…ismGenerator/fix/conda_recipe Small Patches to the Conda Build
…ismGenerator/fix_solvation Update solvent data: (1) fix erroneous viscosities (2) update manuscript citations
…t111 more flexible with lone pairs px. The nodes in the adsorption correction file adsorptionPt111.py were rather restrictive. In most nodes it was specified that the generalR cannot have lone pairs p0. This wasn't noticed as a problem because the R was mostly C in the training data. However, this is not correct. In most cases, the R can also be replaced with O or N. This PR makes the nodes more permissive, by changing the p0 to px whenever it is reasonable. Nodes containing nitrogen were not fixed because Kirk is doing a complete overhaul of the nitrogen adsorption corrections.
…face reaction family trees. Remove reaction path degeneracy adjustments in surface families. These extra nodes and rules were earlier added to remove reaction path degeneracy factors that we now think should be there. This PR removes them. It also therefore simplifies the trees a bit. Only affects surface (catalysis) reaction families.
…ismGenerator/update_correction Update of ccsd(t)f12/augccpvtzf12
…ismGenerator/fix_primary_H2O2_fix fixed irreversible reactions from table 2 of Konnov 2015, X2 and X3
…ismGenerator/update_artifacts_to_v4 Update CI artifact actions to v4
…face_dissociation_vdW_forbidden_N Forbid charged nitrogen species from breaking to prevent AtomType error on N++ species
Elliott SN, Mulvihill CR, Ghosh MK, Curran HJ, Klippenstein SJ. Systematic exploration of the thermochemistry for a set of peroxy hydroperoxy-alkyl radicals. Proceedings of the Combustion Institute. 2024;40(1-4):105618-. doi:10.1016/j.proci.2024.105618
…iott_OOQOOH Add thermo entries from Elliott OOQOOH paper
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